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README.md

@@ -13,6 +13,8 @@ short_description: Cross-disciplinary methodology for complex systems
 
 A systematic visualization methodology for analyzing complex systems across disciplines using Mermaid Markdown and a universal five-color code.
 
+Complex systems across biology, chemistry, and physics exhibit remarkable similarities in their organizational principles despite operating at vastly different scales and domains. Traditional analysis methods often remain siloed within specific disciplines, limiting our ability to identify common patterns and computational logic that govern system behavior. Here, we present the Programming Framework, a systematic methodology that translates complex system dynamics into standardized computational representations using Mermaid Markdown syntax and LLM processing.
+
 ### Purpose and Goals
 
 The Programming Framework project aims to advance the use of Mermaid Markdown syntax and Large Language Models (LLMs) to create standardized, color-coded flowcharts representing complex processes across all academic disciplines. By providing a universal methodology for translating system dynamics into computational representations, this framework enables systematic comparison and pattern recognition across traditionally separate fields including biology, chemistry, physics, computer science, and mathematics. The project builds upon three decades of computational biology research and demonstrates how modern AI tools can democratize complex system analysis, making sophisticated visualization accessible to researchers, educators, and students worldwide.

chemistry_examples.html

@@ -604,16 +604,6 @@ graph TD
         <p>This collection demonstrates the computational nature of chemical processes and systems</p>
         
         <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
-        
-        <div style="margin-top: 3rem; padding: 2rem; background: #f8f9fa; border-radius: 8px; border-left: 4px solid #007bff;">
-            <h3 style="margin-top: 0; color: #007bff;">Contact Information</h3>
-            <p style="margin-bottom: 0.5rem;"><strong>Gary Welz</strong></p>
-            <p style="margin-bottom: 0.5rem;">Retired Faculty Member</p>
-            <p style="margin-bottom: 0.5rem;">John Jay College, CUNY (Department of Mathematics and Computer Science)</p>
-            <p style="margin-bottom: 0.5rem;">Borough of Manhattan Community College, CUNY</p>
-            <p style="margin-bottom: 0.5rem;">CUNY Graduate Center (New Media Lab)</p>
-            <p style="margin-bottom: 0;"><strong>Email:</strong> gwelz@jjay.cuny.edu</p>
-        </div>
     </div>
 </body>
 </html>

mathematics_processes.html

@@ -389,8 +389,6 @@ graph TD
     style T3 fill:#51cf66,color:#fff
     style U3 fill:#51cf66,color:#fff
     style V3 fill:#51cf66,color:#fff
-    style AA3 fill:#51cf66,color:#fff
-    style BB3 fill:#51cf66,color:#fff
     style B3 fill:#74c0fc,color:#fff
     style D3 fill:#74c0fc,color:#fff
     style F3 fill:#74c0fc,color:#fff
@@ -406,14 +404,10 @@ graph TD
     style HH3 fill:#74c0fc,color:#fff
     style II3 fill:#74c0fc,color:#fff
     style JJ3 fill:#74c0fc,color:#fff
-    style EE4 fill:#b197fc,color:#fff
-    style FF4 fill:#b197fc,color:#fff
-    style GG4 fill:#b197fc,color:#fff
-    style HH4 fill:#b197fc,color:#fff
-    style KK4 fill:#b197fc,color:#fff
-    style LL4 fill:#b197fc,color:#fff
-    style MM4 fill:#b197fc,color:#fff
-    style NN4 fill:#b197fc,color:#fff
+    style OO3 fill:#b197fc,color:#fff
+    style PP3 fill:#b197fc,color:#fff
+    style QQ3 fill:#b197fc,color:#fff
+    style RR3 fill:#b197fc,color:#fff
                     </div>
             
             <div style="margin-top: 1rem; display: flex; flex-wrap: wrap; gap: 0.5rem; justify-content: center;">
@@ -525,10 +519,6 @@ graph TD
     style DD4 fill:#74c0fc,color:#fff
     style II4 fill:#74c0fc,color:#fff
     style JJ4 fill:#74c0fc,color:#fff
-    style EE4 fill:#b197fc,color:#fff
-    style FF4 fill:#b197fc,color:#fff
-    style GG4 fill:#b197fc,color:#fff
-    style HH4 fill:#b197fc,color:#fff
     style KK4 fill:#b197fc,color:#fff
     style LL4 fill:#b197fc,color:#fff
     style MM4 fill:#b197fc,color:#fff
@@ -668,16 +658,6 @@ graph TD
         <p>This collection demonstrates the computational nature of mathematical processes and systems</p>
         
         <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
-        
-        <div style="margin-top: 3rem; padding: 2rem; background: #f8f9fa; border-radius: 8px; border-left: 4px solid #007bff;">
-            <h3 style="margin-top: 0; color: #007bff;">Contact Information</h3>
-            <p style="margin-bottom: 0.5rem;"><strong>Gary Welz</strong></p>
-            <p style="margin-bottom: 0.5rem;">Retired Faculty Member</p>
-            <p style="margin-bottom: 0.5rem;">John Jay College, CUNY (Department of Mathematics and Computer Science)</p>
-            <p style="margin-bottom: 0.5rem;">Borough of Manhattan Community College, CUNY</p>
-            <p style="margin-bottom: 0.5rem;">CUNY Graduate Center (New Media Lab)</p>
-            <p style="margin-bottom: 0;"><strong>Email:</strong> gwelz@jjay.cuny.edu</p>
-        </div>
     </div>
 </body>
 </html> 

physics_processes.html

@@ -648,16 +648,6 @@ graph TD
         <p>This collection demonstrates the computational nature of physical processes and systems</p>
         
         <p>Each flowchart preserves maximum detail through optimized Mermaid configuration</p>
-        
-        <div style="margin-top: 3rem; padding: 2rem; background: #f8f9fa; border-radius: 8px; border-left: 4px solid #007bff;">
-            <h3 style="margin-top: 0; color: #007bff;">Contact Information</h3>
-            <p style="margin-bottom: 0.5rem;"><strong>Gary Welz</strong></p>
-            <p style="margin-bottom: 0.5rem;">Retired Faculty Member</p>
-            <p style="margin-bottom: 0.5rem;">John Jay College, CUNY (Department of Mathematics and Computer Science)</p>
-            <p style="margin-bottom: 0.5rem;">Borough of Manhattan Community College, CUNY</p>
-            <p style="margin-bottom: 0.5rem;">CUNY Graduate Center (New Media Lab)</p>
-            <p style="margin-bottom: 0;"><strong>Email:</strong> gwelz@jjay.cuny.edu</p>
-        </div>
     </div>
 </body>
 </html>